Sonic: Chaos and Harmony
by Shadotaku
Summary: Thwarting Eggman's latest scheme didn't go exactly as planned, as Sonic and friends vanish without a trace! In another world, a green flash erupts across the sky, as the Elements of Harmony are thrust into their biggest adventure yet. This time, it could be more than just ONE universe at stake! WARNING: Anthro Ponies! Rated for mild L&V, mostly in later chapters.
1. Assault on the Asgard

*sigh* Yes, my first fanfic is a Sonic/MLP crossover. Laugh if you must, but at least read a bit of it before judging. The idea just came to me, then I started expanding on it, gaining some real direction, and before I knew it, I had something I really wanted to write. I just felt like I had to get it on paper-eh, computer screen... You know what I mean -_-'...

Quick warning: this is my first story, so it might be a little rough in some areas. Feel free to point these areas out to me, but don't flame.

Also, quick note: elements from Sonic's universe (mainly Eggman robots) will be based off of the game continuity, not cartoons or comics. Just thought I'd clear that up, seeing as there are SWATbots early on. They're the ones from Dark Brotherhood. Also, Sonic's world will be called Mobius, just because it seems right to me. I honestly don't know if they ever directly state the world's name in the games, but if this raises any inconsistencies, I apologize.

Well, I think I've wasted enough of your time here. Let's get started!

* * *

**I do not claim ownership of anything in this story. Sonic the Hedgehog and My Little Pony are owned by Sonic Team and Hasbro, respectively.**

* * *

SONIC: CHAOS AND HARMONY

_Chapter 1: Assault on the Asgard  
_

If there was a word to describe Doctor Ivo Robotnik, it would be this: persistent. Commonly called by his nickname, Eggman, the not-so-good Doctor seemed to come up with a new plan to pursue the seven all-powerful gems known as Chaos Emeralds on a weekly basis. No matter how many times his plans had been thwarted, he'd always lick his wounds and come back fighting just as hard as ever, with whatever tricks, weapons, or ancient deities he could muster.

This time was no different. Or rather, it was VERY different. Donned in his signature red and black outfit, his trusty goggles fit snugly atop his head with black, circular shades covering his eyes, Eggman cackled to himself with pride from the helm of his newly-built battleship. Truly, this time he believed he'd outdone himself.

"Eggman, you magnificent mastermind! This time you've outdone yourself!" He boasted, stroking his long, orange mustache. "Truly, this plan could only be conceived by a genius of YOUR stature!"

"Erm, Master?" Came a synthetic voice from the ship's speakers.

Eggman's mood soured as he glared at the nearest speaker. "ADAM! I thought I told you to be quiet!"

"I apologize, sir, but I am about to begin the jump calculations, and your repeated ego-stroking is beginning to get distracting."

Eggman groaned to himself. True, installing an on-board AI in his new "Egg Asgard" was yet another stroke of genius, but making it fully aware was proving to be a double-edged sword, as ADAM seemed to have an opinion about EVERYTHING.

"Fine," he said defeatedly, "but make sure you let me know when we're fully calibrated."

"Yes sir." With that, the AI signed off. Eggman's grin returned. Here he stood, about to step head-first into his greatest scheme yet. The new Slider Drive he'd designed required quite a bit of fine-tuning, but he could hardly contain his excitement as he prepared to see if it was worth the blood, sweat, and tears. If this plan was successful, every victory he'd had in the past (few and far in-between they were) would seem like child's play.

"_You've truly outdone yourself!_" Eggman whispered once more, "_Truly, truly genius!_"

"Sir!"

"OH, COME ON! YOU CAN HARDLY HEAR ME!"

"Not that, Master." Only then did Eggman note the urgency in the synthetic's tone. "There is a small aircraft approaching us head-on!"

Strangely, the news made Eggman smirk rather than panic. "Let me guess..." He then jokingly raised a hand to his chin. "The Tornado?"

As if on cue, the monitor then displayed the image of a silhouette visible through the cloud bank they'd oh-so-wisely chosen to hide in. Sure enough, that unmistakable X-shaped wing pattern could be seen. "Truly, truly genius, Master."

Eggman chuckled at the AI's joking retort. Looking closer at the image, he noticed an all-too familiar spiky silhouette on what appeared to be the plane's tail. The sight of the figure caused Eggman to grin. "Not even HE can stop me this time." he then turned towards the speaker, once more. "You keep doing what you're doing. I'll handle this!"

"As you wish, doctor." With that, ADAM logged off once more.

Eggman then pressed his finger down on a giant, red button on the console before him. "ATTENTION ALL ON-BOARD FORCES!" The doctor's voice boomed over the ship's mics. "WE APPEAR TO HAVE SOME UNWANTED COMPANY! I WANT ALL FORWARD CANNONS AT THE READY, ANTI-AIR FORCES ON-DECK, AND ALL DRONES DEPLOYED TO INTERCEPT! KEEP THE TORNADO AWAY FROM THIS SHIP AT ALL COSTS!"

The response was immediate, as the screen then displayed a large, red banner reading "ACKNOWLEDGED." The image then switched to several small screens of small fighter planes launching from an open hangar, as well as several turret controls coming online. Another screen popped up, showing several SWATbots armed with long-range weapons moving towards the bridge.

Eggman triumphantly donned his signature grin as he watched his orders carried out across the ship. "Genius," he commended himself. "Truly, truly GENIUS!"

**-o-o-o-**

The thin, high-altitude air rushing through his long, blue quills had to be Sonic's favorite thing about flying. That, or the feeling of the cool cloud vapor against the bare skin of his muzzle and arms. Enjoying these sensations while riding on the only vehicle capable of matching his incredible speed almost made the young hedgehog forget that he was on a mission.

"HEY!" A gruff voice shouted over the Tornado's engine, "I THINK I SEE SOMETHING!" The red echidna pointed his spiked glove towards the clouded image they were rapidly approaching. Snapping out of his euphoria, Sonic focused his eyes on the image.

There was no mistaking Eggman's craftsmanship, but the ship's size nearly made Sonic's jaw drop. "Ship" hardly seemed fitting for such a juggernaut, as it was easily bigger than an entire fleet of Eggman's previous works. In shape, it was similar to his previous Egg Carrier, with a long nose, and a wide deck extending along its length. However, the rear of the ship seemed much heavier, mostly made up of powerful thrusters to propel the craft, with several smaller ones lining the nose to keep it airborne. Sitting atop it all was the ship's massive bridge, which seemed almost city-like in nature, with several elongated facilities coming out of a single, dome-shaped base. In the front was what Sonic could only assume was the command center, seeing as it was a giant metal structure in the shape of Eggman's head, with two giant windows resembling eyes. In color, it was silvery-gray with "EGG ASGARD" printed in big, black letters along its side.

Sonic let out a whistle, barley audible over the plane's engine. "I gotta hand it to old Egg-head: he never stops making things interesting!"

"TAILS!" Knuckles the Echidna shouted to the two-tailed fox in the pilot's seat in front of him. "I CAN SENSE THE MASTER EMERALD'S ENERGY COMING FROM THAT SHIP!"

Tails nodded in confirmation. Once again, it seemed like Eggman was up to his old tricks. It had been a while, but after months of being quiet, it was only a matter of time before he pulled something like this. Stealing the Master Emerald was usually the first phase to his plans, hoping to harness the boundless energy it contained for whatever invention he'd cooked up. So really, it was no surprise when the Emerald's reluctant guardian reported that it had been stolen.

"YOU REALLY NEED TO GET BETTER AT GUARDING THAT THING!" Sonic chuckled from his perch on the plane's tail.

"BITE ME, HEDGEHOG!" Knuckles snapped.

"FOCUS, YOU TWO!" the two-tailed fox shouted back. "IT LOOKS LIKE WE HAVE COMPANY!"

The two bickering rivals looked ahead to see a small squadron of Egg Fighters coming at them. The modified Egg Gliders were equipped with a wide wingspan spreading out from their chassis, which resembled the disembodied torso of a SWATbot, but more streamlined with a powerful thruster jutting from the back. Each fighter was equipped with dual rotating turrets on their underside, aimed to kill.

With a playful smirk, Sonic grabbed on to his perch tightly. "THINGS ARE ABOUT TO GET INTENSE!" Knuckles re-tightened his harness, content to leave the dog-fighting to Tails.

The fighters shot first, a flurry of rapid laser fire whizzed past the Tornado's frame as Tails nimbly dodged. Tails had to admit, these fighters were better shots than Eggman's usual aerial bots, but there was still nothing that dominated the skies quite like the Tornado. As they fired, Tails corkscrewed out of the way, launching several missiles at the attackers. Three missiles found their mark, as three fighters burst into flaming debris and fell through the clouds. The rest of the fighters scattered, avoiding the remainder of Tails' barrage, but parting their formation just enough for the Tornado to slip past them.

As the small, red plane slipped past its foes, Sonic saw his opportunity. In a move that could only be called suicidal, Sonic leaped off the back of the Tornado, and towards the nearest fighter. He then curled into a ball, as some unknown force propelled him at his target, striking the craft with enough force to knock it out of the sky. He then performed his signature Homing Attack on three more fighters, sending them all plummeting into the cloud bank.

Almost as if he'd practiced, the blue hedgehog then landed perfectly back on the plane, giving a thumbs-up to his friend in the pilot seat. Tails returned the gesture with a smirk. He knew better than to worry about Sonic when he tried something this reckless.

Now, came the tricky part. With the remaining two fighters behind him, Tails would need someone to cover the Tornado's rear. "KNUCKLES!" He shouted, "IT'S ALL YOU!" With that, he pulled a large, black lever on the right side of his dash.

Knuckles was somewhat surprised as his chair rotated around, a joystick and a monitor appearing before him. Thankfully, Tails had briefed him on this, beforehand. Technology usually wasn't the echidna's area of expertise, but luckily, Tails had kept the briefing simple, by giving him one action and two buttons to memorize.

Grasping the joystick before him, Knuckles swiveled the mechanism until one of the remaining fighters appeared on the monitor. Pulling the stick's primary trigger, Knuckles fired the small rotary turret on the back of the ship, taking the fighter down with one quick burst.

Knuckles smirked triumphantly. "Hey, this is easy!" turning the joystick once more, Knuckles took the remaining fighter down in a manner similar to the first. "WE'RE ALL CLEAR!" he shouted towards the cockpit.

"NOT QUITE!" Sonic shouted in response, "THAT WAS JUST THE WELCOMING PARTY!" Sure enough, even more squadrons of ships began appearing, several among them seeming to be fitted with missile launchers.

Not wasting a second, Tails pushed the steering wheel forwards. "EVERYBODY HANG ON TO SOMETHING!" he shouted. With barely enough time to react, Sonic's grip on the body of the plane tightened to the point of making his hands hurt as the Tornado blasted towards the dreadnought at full throttle.

Eggman's troops instantly lost sight of the plane as it breached their formation, piercing through towards the Asgard with a sonic boom.

**-o-o-o-**

Back in the cockpit, Eggman watched the plane's speedy approach. Luckily, he'd anticipated this, as SWATbots equipped with surface-to-air weaponry were already lining up along the deck. Eggman had to pat himself on the back for thinking so far in advance. It was truly, truly gen-

"Master?"

"I DIDN'T EVEN SAY IT, YET!"

"N-no, not that, sir," the nervous-sounding AI clarified, "there appears to be a strange energy fluctuation within the Master Emerald Core." A large, 3D hologram of the ship appeared before Eggman, a faint, red glow emanating from the core, indicating an anomaly.

Eggman's brow furrowed. "Give me security footage." He ordered.

"There is none, sir." A static-filled screen then popped up to emphasize ADAM's point. "All monitoring devices appear to have been disabled."

Eggman grumbled in agitation. How dare some mystery force show up at the last minute to foil his truly, truly genius master plan? "I'll look into this," he declared. "In the meantime, I want all your attention divided between calibration process and monitoring the situation here. If the Hedgehog makes it on board, you have my permission to go to Defense Plan B, understood?"

"Perfectly, sir." The AI responded. With that, Eggman's control seat detached from the monitors, separating into his iconic hovercraft, the Egg Mobile. Wheeling the Mobile around, Eggman proceeded out the large, sliding doors behind him and began making his way to the Core.

**-o-o-o-**

More fighters burst into flame as Sonic leaped off of them, once again landing perfectly on the Tornado. He directed his gaze downward to see that they were now flying across the ship's long deck. _Alright!_ Sonic thought to himself, _We're making record time!_

As Sonic silently congratulated their progress, he couldn't help but notice Knuckles had stopped firing at the ships behind them. Looking down, he saw the red echidna with a blank expression, seeming to stare off into space.

"YO, KNUX!" Sonic shouted. No response. "EARTH TO KNUCKLEHEAD! YOU THERE?"

It seemed being called "Knucklehead" was enough to get the echidna's attention, as he shook his head and looked back up at Sonic. "Sorry," he said, deciding to pardon the insult, "I just thought I felt... Something."

"WHAT?!" Sonic cupped a hand to his ear as he struggled to hear Knuckles' words over the roaring wind.

A vein appeared on Knuckles' head. "I SAID-"

"HEADS UP!" Tails shouted. Knuckles and Sonic both turned their attention forward to see an entire platoon of SWATbots lining the deck of the ship, each one armed with a large missile pod. The platoon opened fire as the heat-seeking missiles all changed direction, homing in on the Tornado. "KNUCKLES, DEPLOY DECOY FLARES, NOW!" Tails commanded.

"THE WHAT?!" A light bulb then went off in Knuckles' head as he remembered Tails' quick instruction from earlier. "OH, RIGHT!" He then pressed the large, red button on the top of the joystick before him.

With precision timing, Tails made the Tornado perform a complete 180, turning its backside towards the approaching missiles as a flurry of bright fireballs were released from the tail. The majority of the missiles were thrown off by the decoys, swerving into them before detonating harmlessly in mid-air. A few missiles seemed to survive, though, as Knuckles then began shooting at them with the rear turret.

"I THINK THIS IS AS CLOSE AS WE CAN GET!" Tails shouted.

With a confident smirk, Sonic responded, "THEN I GUESS THIS IS MY STOP!" Sighting a nearby fighter, Sonic once again abandoned the relative safety of the Tornado to leap towards the small drone.

"SONIC!" Tails shouted, more out of reflex than concern, as he had faith in his big brother-figure to know what he was doing.

Instead of performing a Homing Attack, Sonic landed on the flying mech's back, planting both feet firmly on the enemy's wings and grabbing the top of its head with both hands. "Going my way?" he asked sarcastically. He then pulled on the robot's head with all his might, forcing the drone to alter its flight path and turn towards the bridge.

Tails grinned as Sonic flew away on his makeshift transport. "BE CAREFUL SONIC!" He shouted, hoping the hedgehog would hear. "AND GOOD LUCK!"

Knuckles, however, was deep in thought. What was that feeling earlier? It had felt so familiar. He suddenly found himself suspecting that Sonic and Eggman weren't the only ones on the Asgard.

**-o-o-o-**

Eggman floated through the core chamber, carefully observing his surroundings. A pair of large Shield Troops accompanied him, their hulking figures making him feel protected.

However, seeing as there was nothing in this room except the Master Emerald glowing brightly in its glass containment sphere, he began to doubt there was anything to be worried about. Still, he knew from experience that strange energy readings are nothing to be taken lightly when Emeralds are concerned, so his nerves were still on high alert.

"Doctor."

ADAM's sudden voice was enough to make Eggman jump. "EEEEEEK!"

"... Did you just scream like a woman, sir?"

Eggman shook off his initial shock. "BLAST IT ALL, WHAT DO YOU WANT?!"

"I thought you would like to be informed that Sonic has hijacked an Egg Fighter and is making his way towards the bridge." Eggman couldn't help but give a light chuckle at the resourcefulness of his old foe. "Defense Plan B has been deployed."

"Excellent." Eggman grinned sadistically. "How much longer until we're prepared for the jump?"

"Calibrations will be complete in mere moments, sir." Eggman nodded in satisfaction. "How go things on your end?"

"It appears to be a fluke. I'll double-check for energy leaks, then return to the bridge." ADAM acknowledged its master's update before returning to its task. Eggman was about to examine the nearby machinery, when he saw something move out of the corner of his eye. Due to the room's dull, green illumination, it was hard to make out anything specific, but sure enough, Eggman gad seen one of the many shadows in the room move. "HALT WHERE YOU ARE!" Eggman commanded, his guardians shining light on the intruder.

Eggman only had time to gasp as the intruder was revealed, as two red bolts of energy flew past him and struck his two escorts in the chest, piercing their thick hides before the bots could even arm their weapons. Still, the lights had done their job, revealing the identity of this uninvited guest. Seeing no point in hiding, the figure emerged from the darkness, his metal boots clanging against the floor as he stepped into the glow of the Emerald. His upturned black and red quills swayed behind him, as his right hand crackled with energy, a glowing, green gem held firmly in his right.

Eggman smiled in false courtesy at his favorite traitor. "Hello, Shadow. It's been too long."

The dark hedgehog smirked at the old man. "Hello, Doctor. So where are we headed today?"

Eggman's smile widened into something sinister. "Oh, what a fantastic question. Allow me to fill you in, old friend..."

**-o-o-o-**

In all his years of fighting Eggman, Sonic found nothing gave him a rush quite like crashing into the deck of the doctor's latest dreadnought. Needless to say, doing so on a modified SWATbot was quite the experience. Ditching the scrapped robot behind him, Sonic sprinted forwards at top speed, a sonic cone forming around him as he ran.

_Dang,_ Sonic thought to himself, _Eggman's really outdone himself this time! I might even get a workout!_ Indeed, the length of the ship seemed to go on for miles. Even at his top speed, Sonic realized it may take him several minutes to reach the bridge. _What the heck could Eggman be planning with a ship like THIS?_

Before he could question the subject further, a missile soared past him. The anti-air rockets from earlier were now aimed directly at him. Of course, Sonic just grinned in the face of the oncoming danger. "Here we GO!"

The next rocket was aimed directly at Sonic's face, but Sonic avoided the projectile by curling into a ball and using his momentum to roll across the ground. More missiles were fired directly at the spin-dashing hog, but each one only hit the deck as their target skillfully weaved past each and every one. Soon, more fighters from above joined in the assault, as they aimed at the tiny, blue ball with lasers and missiles, but they weren't any more successful.

It didn't take Sonic long to reach the front of the formation of SWATbots, his spin-dash impacting the frontal robot's side with enough force to spin the robot around, firing its already primed missile into the squadron behind it. Sonic seemed to be caught in the explosion, himself, until he emerged from the blast, slightly singed and flying at top speed.

He found himself once again landing on an unsuspecting SWATbot, the mech thrown slightly off-balance and firing a rocket into the air. Sonic made sure to take advantage of his position, bending over and taunting the aerial troops with his blue posterior. Although not capable of being insulted by the vulgar gesture, the drones took advantage of Sonic's momentary stillness to launch a full-force barrage at their target. Sonic leaped off the SWATbot with perfect timing, the resulting explosion decimating the SWATbot platoon and propelling Sonic forward through the air.

Sonic landed and wasted no time in regaining his speed, still dodging and weaving as he avoided fire from the air squadron. _Now how to take care of those?... _he thought.

The answer to Sonic's question came sooner than he thought. Now free of the threat of surface-to-air missiles, the Tornado swooped in from above, taking out the remaining fliers with its vulcan cannon. Coming in low, Tails gave Sonic a thumbs-up. Sonic nodded and returned the gesture, then increased his pace across the deck as Tails returned to the sky to keep the troops busy.

Surprisingly, the action with the SWATbots seemed to increase Sonic's pace, as he seemed to be nearing his destination much sooner than he thought. Just as he was beginning to wonder how he was going to get in, the hangar before him began to open. "Heh! Laying out the red carpet, Eggman?" Sonic asked no one in particular, "You're too kind!"

Sonic rushed towards the hangar, attempting to make it inside before he was noticed. However, just as the door had opened enough to let him through, Sonic was caught off-guard as a blue and yellow blur rammed into him. Sonic's record pace was ground to a halt as he was knocked several feet back by the powerful blow. He landed hard on his back, groaning in pain from the impact.

"Interception successful." Came a monotone, synthetic voice. "'Defense Plan B' initiated."

Sonic painfully pushed himself up, as he looked upon his attacker. There was no mistaking the similarity between the attacker and himself, both of them sharing similar head spikes and color schemes. The attacker, however, was clearly mechanical, as his optics burned a sinister red, and a powerful jet turbine hummed in his chest. The doppelganger also seemed to be equipped with several upgrades, as he was much bulkier, and stood nearly a full head taller than the organic hedgehog. Still, if that hit from before was any indication, there was no denying his speed. A yellow trim also seemed to accentuate most of his features.

Shrugging off his pain, Sonic stood up and began dusting himself off. "Well, well. Long time no see, Metal. And here I thought you'd been sent to the scrapheap, by now." Receiving no response, Sonic grinned as he looked over his old adversary's impressive new form. "And it looks like you're new and improved, to boot!" Sonic then hunched over and assumed a cross between a fighting and running stance. "Whaddya say we see what the new you is made of?"

Metal Sonic accepted his copy's challenge, the turbine on his back flaring to life. Sonic ducked into his Spinball form as he spun rapidly, building up speed and power. The two then charged at each other, their clash powerful enough to create a shock wave across the deck.

**-o-o-o-**

"So? What do you think?" Eggman finished. Years of experience had taught Eggman that the self-proclaimed "Ultimate Life Form" was easier reasoned with than fought, so he'd spent the last several minutes explaining his plan to Shadow, hoping the hedgehog would see reason. If not, the conversation still proved a good way to stall for time. "Genius, right?"

After patiently listening with his arms crossed, Shadow chuckled. "I have to admit, you've outdone yourself, Doctor." Eggman beamed at the compliment. "This is by FAR the dumbest thing you've ever done!"

Eggman looked almost hurt at the change in tone. "Oh, come now, Shadow my boy! Surely you must see the potential of this plan!"

"Potential? You're talking about opening an inter-dimensional rift with no idea where you'll end up! The only potential I see is for suicide."

"Ah, but that's where you're wrong, my dear Shadow. For you see, I have my new EGG ASGARD, and THIS!" He then gestured to the Master Emerald behind him. "You saw it yourself, Shadow. The Twilight Cage; a void prison for the most dangerous races of not just this, but several different planes of reality! And still, you and your little troop of do-gooders managed to win them over to your side and form a rebellion! If a handful of goody-two-shoes could sway such powerful forces, it should be a cinch for one such as myself!"

Again, Shadow chuckled. "If we're comparing your achievements to Sonic's, I suggest you double-check the scoreboard. Have you even questioned what might happen if your new 'army' doesn't appreciate a hostile takeover?"

"Oh, don't you worry about that, Shadow. I've taken into account the risks and provided several contingency plans, just in case. Besides, any risk is worth getting away from that blasted hedgehog! You can relate, right?"

"I suppose," Shadow said with a smirk.

"So what do you say?" Eggman extended his hand towards the ebony-furred hog. "Care to join me?"

Shadow looked at the doctor's outstretched hand for a moment before batting it away. "As much as I'd love to see this plan blow up in your face, I can't let you go through with this." His palm then began to crackle with energy. "This is the end of the road, Doctor!"

Eggman began to look terrified, but suddenly the Master Emerald behind him began to shine radiantly. Shadow had to shield his eyes, only to notice the energy fade from his hand without him willing it to. He grasped his wrist and tried to reignite the spark, but nothing happened. Eggman watched, puzzled, when suddenly ADAM's familiar voice returned.

"Doctor, the calibrations are complete. The Master Emerald's energies are fluctuating in preparation for dimensional jump. I recommend leaving the vicinity of the Emerald IMMEDIATELY!"

Realizing that the Master Emerald's power would cancel Shadow's Chaos powers, Eggman turned to his now powerless opponent with a triumphant smirk. He then pressed a button on the Egg Mobile, causing a pair of large, robotic arms to drop down from the ceiling. They appeared to be carrying some kind of mechanism with two, bulky limbs attached to it. On each limb appeared to be several assorted weapons, ranging from gattlnig guns, to a missile pod, and even a pair of maces. The mechanism attached to the back of the Egg Mobile, where it then wrapped around the small semi-sphere, locking in place to resemble some kind of battle armor with "EGG BRAWLER" printed across the front. The assorted weapons then began to fold inside of the large limbs they were attached to, until they resembled a large pair of arms with three-pronged claws for hands.

"You heard him, Shadow..." The mechanical arms that carried the upgrade ascended back into the ceiling once the upgrade was complete. A protective glass shield then covered Eggman's cockpit as the robot's clawed hands rose up in a defensive stance, before receding into the wrists to be replaced by a pair of maces.. "GET OUT!"

**-o-o-o-**

Loud crashes echoed across the deck as Sonic and Metal's attacks collided. The two were nothing but two blurs of blue as they continued to clash at the speed of sound. The nearby SWATbots just seemed to be watching the spectacle from a safe distance, no longer sure of what to shoot.

Eventually, the fighters became visible once more. Metal Sonic had a few scuffs and dents, but overall looked no worse for wear. Sonic, on the other hand, was clearly reaching his limit. _Dang,_ Sonic thought as he gasped for breath, _I guess those upgrades really aren't just for show._

Metal was about to charge again, when suddenly, something distracted him. It was a large siren, blaring across the ship as the large eyes of the bridge began to flash red. He glared back at Sonic one last time before - almost reluctantly - walking back towards the hangar.

Sonic stood, puzzled for a moment, but the sound of assorted metal clanging behind him got his attention. Turning around, he was met with the shocking sight of a SWATbot stampede heading his way. Sonic instinctively ran in the opposite direction. Only then did he thought occur to him that he was running straight into an open hangar that would soon be filled with deadly, panicked SWATbots. Quickly deciding an alternative route was needed, Sonic began looking for another route.

"SOOOOOONNNNNIIIIIIIC!"

Sonic followed the cry to see the Tornado swooping in from above, Tails applying full throttle while Knuckles leaned out the side with an outstretched hand. Sonic changed course, jumping up to catch the echidna's spiked glove just in time to be swept out of the way of the robot stampede. Knuckles grinned proudly at his save. "NOW WHAT WAS THAT ABOUT BEING A LOUSY GUARDIAN?" Sonic simply smiled and gave a thumbs-up with his free hand in response.

After being hoisted up to his usual spot on the Tornado's tail, Sonic looked down to see a massive number of robots pouring into all open hangars, both from the deck and sky. "WHADDYA THINK'S GOING ON DOWN THERE?!" Sonic questioned.

"I DON'T KNOW," Knuckles responded, "BUT I CAN SENSE THE MASTER EMERALD'S ENERGY ACTING UP! I THINK EGGMAN'S ABOUT TO PUT HIS PLAN INTO MOTION!"

"NO KIDDING! HOW ARE WE GONNA STOP HIM, NOW?"

"LOOK!" Tails shouted. "SOMETHING'S HAPPENING!"

Sure enough, something strange was going on inside the large, dome-shaped area of the Asgard. Several small hatches were opening along its side, a radiant, green light pouring out. "THAT'S IT!" Knuckles shouted, "THE MASTER EMERALD'S IN THERE!"

"TAILS, GET ME TO THE BRIDGE!" Sonic commanded.

Despite his faith in his best friend up until now, this was the time for Tails to be worried. "SONIC, I DON'T THINK THIS IS A GOOD IDEA!"

"THERE'S NO TIME TO WORRY ABOUT THAT, TAILS! WE GOTTA MOVE!"

Tails looked back at Sonic with concern. "BUT SONIC-"

"HE'S RIGHT, TAILS! THERE'S NO TIME!" Knuckles pointed towards the dome again, where the green glow was beginning to spread across the body and envelop the entire ship.

Realizing his friends' point, Tails gave a determined nod before altering his flight path. Without slowing down for even a second, the Tornado looped around and flew straight for the bridge.

Inside, the navigation robots could only scramble around in their seats in sheer terror as the Tornado approached. Before any of them could have time to escape, the small plane burst through the rightmost window, bringing in a shower of broken glass and freezing wind. The Tornado crashed into a large computer monitor as Sonic was flung from his spot aboard the tail, and into the far wall.

After bouncing back and hitting the ground, Sonic stood up, rubbing his throbbing skull. "Ugh... Not exactly what I had in mind... But I guess it worked!" Letting his vision straighten out, Sonic looked around the room, observing several monitors, gauges, terrified nav-bots on the edges of their seats, _but no Eggman..._

Seeming to read his friend's mind, Tails hopped out of the wrecked plane and walked over to give his two cents. "Looks like Eggman's not here." The young fox put a hand to his chin in thought for a moment. "I'll bet anything he's near the core to oversee things!"

"Sounds like a heading to me! Let's go!" With that, the dynamic furry duo prepared to take off, but a nearby groan caught their attention.

The two of them turned around to see Knuckles, seeming to be stuck in his tightened harness. "Don't worry about me, I'll catch up." He assured them, cursing a little under his breath. "Just go get the Emerald back!"

Sonic gave Tails a questioning glance. "I'll give him a hand," Tails said, "you just, uh... Do what he said! We'll be right behind you!"

Giving a quick nod, Sonic rushed out the nearby doorway, into the interiors of the ship. Tails, on the other hand, worked his way over to Knuckles, who was still struggling with his belt. "Hang on, Knuckles," the fox said, "it looks like it's caught on something."

Knuckles stopped squirming to shoot Tails a lazy glare. "Really. No kidding. Wow, Tails, you're such a genius." His voice seethed with sarcasm.

Tails glared back at him. "Do you want my help, or not?" He took Knuckles' rolling his eyes as a "yes" and proceeded to get to work. It was really proving to be harder than he'd anticipated.

"What the heck did you make this thing out of, Tails?"

Tails laughed sheepishly at his own foresight coming back to mess with him like this. "Well, see, I wanted them to be safe, so I devised a way to apply subatomic-"

Tails' explanation was cut off, by the sounds of more blaring sirens. "BREACH DETECTED! BREACH DETECTED!" came a synthetic voice, "EVACUATE THE BRIDGE IMMEDIATELY!" The room was bathed in red light as all the still somewhat unnerved nav bots quickly ran for the exit.

"That doesn't look good." Knuckles observed. The two of them then watched as a giant steel plate slid down, completely closing off their only exit. "THAT looks worse!" He then began redoubling his efforts to help Tails get him free.

**-o-o-o-**

Eggman fired the Egg Brawler's gatling guns at his speedy opponent. Though he was robbed of the power the Chaos Emerald granted him, Shadow was still not a force to be taken lightly. His jet-propelled hover-shoes allowed him to glide across the ground and perform midair maneuvers that made him very hard to hit.

The bullets pelted the ground where Shadow stood seconds before, but the black hedgehog had vanished from sight. "You can't hide from me, Shadow!" Eggman threatened, scanning the room, "It's beneath you, old friend!"

The hedgehog in question was well hidden behind one of the room's generators. Shadow knew Eggman wouldn't dare open fire on such a vital piece of equipment, but it was only a matter of time until he looked there. Shadow glared in agitation at the powerful gem in his hand, now rendered dead weight. There had to be a way to still use it to his advantage, there just had to be!

"WARNING!" came ADAM's voice over the ship's speakers. "INTER-SPACE JUMP IS ABOUT TO BEGIN! ALL PERSONNEL, EVACUATE THE CORE AREA IMMEDIATELY!" Eggman shrugged off the AI's warning as he continued to search the room. "THIS MEANS YOU, MASTER!"

With a dejected sigh, Eggman piloted his floating mech towards the room's entrance. "Alright, Shadow, be that way if you must." He then swapped out his gatling gun for a three-pronged claw from earlier, using its slender digits to punch in a number on the keypad, causing the doors to open with a hiss. "Just know that this is your only chance to run."

The enhanced Mobile then proceeded out of the room, only to be met with the sole of a bright red sneaker traveling at what had to be over a hundred miles per hour. The force of the blow didn't crack the glass dome at all, but it was strong enough to send the hovercraft flying back into the chamber, slamming hard into the Master Emerald's container. After being roughly shaken around the cockpit, Eggman sat upright to look his blue-furred, long-time nemesis in the eye as the door hissed shut behind him. On his face, the hedgehog wore that cocky grin that the doctor had come to despise. "Who said anything about running, EGGMAN?"

"Sonic..." Eggman grumbled. In hindsight, he probably should have seen this coming sooner or later. Suddenly, a thought occurred to Eggman as he quickly turned the mech around, examining the glass chamber behind him. Sighing in relief to find it still intact, he then spun around to face his nemesis once more. "YOU FOOL! Do you have ANY idea what you ALMOST DID?!"

Sonic's grin remained wide as ever. "You mean kick your butt for the umpteenth time? Sorry, Eggman, but I don't do 'almost!'"

"NO! Not here, you little IMBECILE!" he then used the mech's arms to gesture to the large container housing the Master Emerald, causing Sonic to raise an eyebrow. "This container is all that's keeping the Master Emerald's energies in check! If this so much gets a crack, the power fluctuations will become unstable, causing the Slider Drive to overload, and then WHO KNOWS what will happen! We could be atomized in the blink of an eye, scattered like dust in the wind. Or we could be flung to the far reaches of time and space, itself, helpless to do anything but waste away into-"

"Oh hey, Shadow! When did you get here?" Eggman halted mid-sentence to see Sonic was completely ignoring his speech and seemed to be looking above him.

Eggman followed Sonic's gaze, rotating in his seat and looking upwards. Sure enough, Shadow had reappeared, standing several feet above him atop the Master Emerald's glass bubble. The ebony hedgehog then gave the doctor an intense glare, staring him down as he raised the lifeless Chaos Emerald in his hand. Surely, he wasn't about to...

"SHADOW, NO!" Eggman shouted in panic, but there was nothing he could do. Even Sonic couldn't react fast enough to stop the dark hedgehog as he swung his arm downwards, the sharp tip of the Emerald's base shattering the glass container on impact.

In an instant, everything erupted into pure chaos. Green wisps of light flowed from the shattered bubble, quickly swirling around and filling the room completely. A loud, ethereal wail filled the room, as if the Master Emerald itself seemed to be screaming in agony. The large gemstone almost glowed with the intensity of the Sun, forcing everyone in the room to shut their eyes and cover their ears.

"SHADOW, YOU FOOL!" Eggman shouted as loud as he could, "YOU'VE DOOMED US ALL!"

**-o-o-o-**

Outside, the green glow the trio of heroes noticed earlier had almost completely enveloped the Egg Asgard. Suddenly, the Asgard's dome structure began to glow ten times brighter, as an eerie, almost wail-like noise erupted from the ship, along with several long, glowing, ethereal wisps.

Within moments, the radiant light had expanded, making the entire rear half of the ship look like a miniature sun. The light continued to grow as the wailing noise grew louder. Soon enough, the entire ship was enveloped in a ball of radiant green, wisp-like lights dancing around it.

Suddenly, the wail burst into an ear-piercing screech, as a brief flash of light filled the sky. When the light faded, everything was gone. No lights, no eerie noise... No Egg Asgard, and no heroes.

* * *

WHOO, MAN! I did NOT intend for this chapter to be this long! I literally spent DAYS writing this!

So, yeah that's the first chapter of Chaos & Harmony. Don't forget to rate and review, and don't hesitate to be honest; I love a good critique.

And yes, I know there was a severe lack of MLP content in this chapter, but never you fear, my dear Brony readers, things are gonna get Equestrian next chapter!

- Lates, folks :)

* * *

Questions about this chapter:

**M-Tails-P**: It wasn't my intention to make Shadow sound like the villain. I tried to make him an anti-hero on his own agenda, since well, that's who he is. The reason I made him and Eggman appear to get along at first is because out of all the Sonic characters, Shadow is the most likely to hear Eggman out and reason with him, a fact the doctor knows and has taken advantage of in the past. I thought I made it pretty clear that he still hates Eggman, though. Also the reason for the "Royal Canterlot Voice" was because they're trying to talk over the plane's engines and high-altitude winds. Again, I thought I was pretty clear about that ^_^'.

**Guest1**: Again, I thought I made it pretty clear that Eggman and Shadow are NOT on the same side. I guess I need to get better at this -_-'.

**masterart**: Read and find out :)


	2. A Flash in the Night

Okay, so I figure, for this chapter, I gotta clear up what I meant by "Anthro Ponies." Well, I'm kinda going for a more serious, dramatic, and action-y tone for this story, and well, the 4-legged Ponies we all know and love just didn't seem to fit. So, I tried humanizing them a little more, but not to the point that they're no longer the unique, colorful creatures that they are, just enough that they'll be able to stand upright and not look goofy. Really, pretty close to Sonic's own style, now that I think about it... Huh.

Plus, more humanoid designs means that I can also design unique wardrobes for the characters! Yippee 8D!... That didn't come out quite right...

... ANYWAYS! Here's chapter two! Enjoy!

* * *

**Once again, I claim no ownership to anything used in this story.**

* * *

SONIC: CHAOS AND HARMONY

_Chapter 2: A Flash in the Night_

In the realm of Equestria, the Everfree Forest just outside of Ponyville was a place infamous for its mystery and secrets. It was home to some of the most mysterious and bizarre plants and animals one could ever encounter. As such, the reason why Fluttershy, the most timid, afraid-of-her-own-shadow pony in the world, had chosen to live so close to it was anypony's guess.

In truth, Fluttershy was deathly afraid of the forest and all that lurked within it. However, having ventured into it on more than one occasion (with her friends' motivation) had made her feel a little safer in her own home. Besides, she chose her living place for a reason: the animals. For whatever reason, the large house atop the hill seemed to be quite popular with local fauna of all shapes and sizes, and if there was anything that outweighed Fluttershy's fear, it was her love of all creatures.

The yellow, pink-maned pegasus-morph in question happened to be getting ready for bed at the moment. She'd just slipped on her favorite light-green nightgown, and had already tucked in her pet rabbit, Angel, for the night. Just as she'd slipped under the covers of her own bed and was about to drift away to her dreams, something caught her ears.

It started as a low, almost calming whisper. However soft the sound was, it was enough to make the shy pegasus sit bolt-upright in her bed. As she strained her ears, the sound increased in volume, becoming an almost ethereal, whispering moan.

Fluttershy was now beginning to become afraid. Without a second thought, she immediately dove under her sheets and hugged them tight to her body. She poked her eyes out, only to have them widen in terror as a green glow started to pour through her window, accompanying the terrifying noise.

The poor, scared-out-of-her-mind pegasus shut her eyes tight as the wail erupted into a deafening screech, the a burst of green light erupting from the forest outside. Then, just like that, all was quiet again.

**-o-o-o-**

"Twilight! Come on, Twilight, you have to see this! TWILIGHT!"

The purple unicorn awoke at the sound of her name. She sat up in her bed and pushed her pink-and-purple-striped bangs out of her eyes to see her loyal, scaly companion jumping up and down at her feet. "Ugh... Spike," she said sleepily while rubbing her eyes, "Do you have any idea how late it is? You should be asleep!"

"Never mind that, you gotta HURRY!" The young dragon seemed to ignore Twilight's question as he ran over to the window by her bed. "You're gonna miss it!"

Groaning, Twilight climbed out of her warm sheets, over to Spike's position by the window. "Alright, I'll bite. What's so..." She trailed off as she followed Spike's gaze, "Im... por... tant?..." She honestly had no words for what she was looking at. Beyond the border of Ponyville, the Everfree Forest was GLOWING! An eerie green light shone from within the woods, seeming to fill up the entire night sky.

"This is totally crazy, right?" Spike asked. His tone was somewhat mixed between nervous and excited.

"Very..." was all Twilight managed to say. _I wonder how Fluttershy's doing?_ Twilight couldn't help but worry.

"I wonder how Flutterhy's reacting?" Spike said, almost mimicking Twilight's thoughts. "Man, she's probably SO freaked out!"

"Spike, that's hardly the biggest question ri-"

"She's probably curled up under her bed, by now. She might still be there tomorrow!"

"Spike..."

"Or maybe she shot straight up through the ceiling! HAH!"

"Spiiike..."

"She could've even been abducted by ALIENS! Think about it, Twilight! What else but aliens could make the Everfree Forest glow like tha-"

"Spike, LOOK OUT!" The light glow had suddenly intensified into a radiant burst of light, accompanied by the sound of a distant scream. Twilight barely had time to push her dragon companion out of the way before a glowing object came flying out of the forest and shattered through her window. She clutched the small dragon tightly to her chest as the glass rained down from above, bouncing harmlessly off of her purple pajamas.

After a moment of getting over the shock, Twilight sat up and started looking Spike over. "You alright?" She asked.

"Y-yeah..." Spike replied, "Uh... Thanks."

Twilight gave a glad smile "Don't mention it!" Then, her expression got more serious as she looked out the window. As she expected (or rather, hoped) the Everfree Forest had returned to its dark, peaceful state. "But what WAS that just now?"

Spike's gaze, however, was drawn elsewhere. "Nevermind that," He then pointed over to the smoldering remains of what used to be one of Twilight's many bookshelves. "What about THAT?!"

Looking over, Twilight realized that the object that flew through her window was still glowing bright green in the wreckage of her literature. Extending her hand, Twilight's horn started glowing as she tried to pull whatever it was from the rubble. However, she seemed unable to pull it towards her.

_Strange..._ She thought. She then let go of Spike and walked across the room towards the mysterious object.

"Twilight, DON'T!" the reptile protested, "It could be an alien egg! Or a demon's curse! Or, or..."

"Spike, you read too much Daring Do." _Although, I have to admit,_ she thought as she bent down to pick the curious object up. It was warm to the touch, yet surprisingly cool for something that had just been flying through the air in a green fireball. Other than that, it appeared to be nothing but a glowing, green gemstone. _... This thing is definitely... Odd..._

**-o-o-o-**

Fluttershy opened her eyes, slowly rising from the safety of her sheets. The sky was dark once more, and the mysterious noises had ceased. Now, the only sound that filled the night was the noise of various animals running around in a panic.

Calming her nerves, Fluttershy sighed as she pushed her covers off. She realized what she had to do. "So much for a good night's sleep..." She pushed herself up and grabbed a light jacket off a nearby rack.

In the corner of the room, she noticed that Angel had woken up, and was now shivering with terror in his bed. "Angel, did those lights scare you?" Fluttershy asked her pet with a warm smile. The rabbit straightened up and crossed his arms, as if offended by the suggestion, and shook his head vigorously. Fluttershy giggled as she picked the small bunny up. "That's alright. Mama's scared, too. How about you come with me and we can keep each other company? How does that sound?" The rabbit, now looking very annoyed, simply hoisted himself out of Fluttershy's grip, landing on the ground and walking towards the door. He still kept up his false bravado, as if he was going with her because he wanted to, not because he was scared.

Fluttershy simply smiled and calmly followed her pet outside.

The scene outside was hectic, as several goats, monkeys, and more were running around like chickens with their heads cut off (thankfully, though, all the actual chickens were still in one piece). Even with her unique animal-handling skills, Fluttershy wasn't sure she could calm this scene down.

**-o-o-o-**

The two Poniville citizens weren't the only ones who noticed the disturbance that night. Deep within the Everfree Forest, a shack stood in the middle of a small grove of twisted trees. The shack's sole inhabitant, a zebra-morph known as Zecora, dressed in shaman-like wear with her mane erected into a black-and-white mohawk, had been roused from her late-night meditations by the bizarre lights and sounds.

The spiritual forest-dweller emerged from her humble abode to look for the source of the phenomenon. What she got, instead was a stampede of frightened creatures running by her home, ferocious predators such as basilisks and manticores among them. The last beast to come lumbering by was actually a rather sizable dragon, though it seemed just as terrified as the rest.

Zecora looked off into the forest at the area the animals had come from. She didn't see anything, but her spiritual awareness sent a strange sensation through her body that forced a foreboding chill down her spine.

"Something has filled the forest with fright," she stated, "but what is this thing that goes bump in the night?" Despite the warning signs, Zecora grabbed her shaman's staff and headed deeper into the Everfree Forest, determined to find out what could disrupt a place such as this.

**-o-o-o-**

It felt like hours before Fluttershy was finally able to coax the last animal back into its den. "Now, now, Ms. Bobcat," she told the creature in her usual, soothing tone, "I hope you feel better. You get your rest, and you can apologize to the Raccoon family tomorrow." The feline purred as it curled up, drifting into sleep.

Fluttershy let out an exhausted breath as she looked over her work. Thankfully, no real damage had been done to the animal's homes, and she could ask a certain earth pony friend of hers to help repair the fences, tomorrow. But for now, the pegasus's task was done, and she was finally ready for the sleep she had been oh so dearly looking forward to.

She spread her wings and began floating back towards her house, but was cut off when Angel suddenly appeared between her and the door. The rabbit appeared startled; he was out of his breath and his eyes were widened. "What's wrong?" Fluttershy asked.

Angel then started jumping up and down frantically, pointing repeatedly towards the left. Fluttershy followed his gesture, seeing he was pointing towards the shadows of the Everfree Forest. The timid pegasus felt her heart sink as she looked into the dark trees. She couldn't shake the feeling that whatever had happened a few moments ago had originated from those forsaken woods.

"Oh, you, um..." Fluttershy then began frantically looking around in that direction, searching for anything Angel could've been referring to BESIDES the most horrific place this side of Canterlot. "You want to go to the carrot garden? Well, alright, I suppose a _teensy_ midnight snack couldn't hurt." As she floated towards the garden, however, she felt a slight snag on her behind.

She looked down to see that Angel had grabbed the end of her tail and was shooting her a disapproving look. The agitated rabbit started tapping his foot as if to say "Don't play dumb with me."

Again, Fluttershy began looking for an excuse not to go near the woods. "The coliflour patch, then?" she asked with a hopeful smile. The rabbit smacked his forehead with his free hand, before letting go of Fluttershy's tail and hopping off as fast as he could towards the forest. "Angel! No, wait!" Fluttershy shouted, taking off after her pet.

For such a small rabbit, Angel had impressive leg strength, as he managed to put a significant distance between him and his master. Then again, Fluttershy never was the fastest flier. Whatever the case, Angel reached the edge of the forest and, even as Fluttershy shouted at him not to, he jumped head-first into the overgrowth.

Fluttershy hesitated for a moment, not wanting to set even one hoof into those scary woods. However, she quickly decided that Angel's safety was more important than her own fears. Taking a deep breath, she shut her eyes tight and floated nervously forwards.

After a couple seconds of blind drifting, Fluttershy ran into something hard and fell to the ground with an "Oof!" She looked upwards, rubbing her sore head, to realize that she'd run head-first into a tree. Looking behind her, she realized she had only ventured a couple yards beyond the border. Considering her only encounter so far was with an unfriendly tree, Fluttershy decided, _So far, so good._

"Angel!" She called out, pushing herself up, "Angel, where are you?" Sure enough, the white bunny emerged from the bushes a few feet ahead, motioning for Fluttershy to come over. Deciding there was no point in turning back after coming this far, she once again started flapping her wings and floated over to the little snow rabbit, wondering what could possibly have come over him.

She pushed over the bush to spot Angel waiting for her. He made sure she was watching him before sprinting off to his left, leaving Fluttershy no option but to follow him. "Really Angel, what could-" her words were caught in her throat as Angel stopped a couple feet ahead, motioning to a strange, furry creature the likes of which Fluttershy had never seen. "Oh, my..."

**-o-o-o-**

"...ctor! Doctor, wake up!"

Eggman groaned as he sat up. His head was pounding as his eyes adjusted to his surroundings. He looked to be inside his Egg Mobile, that much was clear, but beyond that...

"Doctor!"

The voice seemed familiar to Eggman, but he couldn't quite place it. "Mommy?..." He asked groggily.

"Oh thank goodness you're alright, sir! You had me worried for a moment."

Suddenly, realization came to the doctor all at once. He recognized where he was! He realized who the voice belonged to! "ADAM!" he shouted, "What just happened? Why does my head hurt so much?"

"Well, master," the AI responded, "I believe it may have something to do with you loosing consciousness after the Emerald Core was ruptured."

All at once, recent events came rushing into Eggman's memory. Shadow, Sonic, the Emerald, all those bright lights, and finally, darkness. "Damn that Shadow!" the doctor cursed, "He nearly killed us all!" He then scanned the room, noticing the Ultimate Life Form was nowhere to be seen. Come to think of it, the room seemed to be devoid of hedgehogs, entirely. "Where did those two go?"

Once again, ADAM was quick with an explanation. "As far as I can tell, sir, it would appear that the jump to another dimension was successful. However, it seems that the last-minute instability of the Slider Drive had dome disastrous after-affects. Sonic and his friends, as well as Shadow, have all vanished, likely scattered to different nearby locations. I suppose the reason you are still here is due to the Egg Mobile and Brawler-upgrade being made out of the same alloy as the rest of the ship."

"I see..." Eggman responded. That DID seem to make sense. After all, he didn't want a single piece of his masterpiece, the Egg Asgard, to be left behind in the jump. So, he'd tested and tested until he found a material capable of withstanding the warping fields generated by the Slider Drive, and then used every ounce he could muster to build the entire ship, as well as all its weapons and troops. "But the jump WAS successful?"

"Well," if the AI were capable it would definitely be sweating right about now. "Yes and no, sir. We DID reach another dimension. However, the mid-jump rupture produced a more disastrous reaction than we'd anticipated."

Eggman did NOT like where this was going. "Disastrous, how?..."

"Erm..." ADAM knew he had to pick his words very carefully. "Well, you see... There's no light way to put this sir: over 60% of the ship is gone."

Eggman's eyes widened so much, they nearly popped out from behind his glasses. "WHAT?!" Not wasting a minute, he raced out of the core room as fast as the Egg Mobile would carry him. When he reached the bridge, he opened a keypad by the door, and entered a code that lowered the blast gate and made the door swish open. What he saw made his jaw drop.

The broken view-port was to be expected. After all, why else would the blast shield have been up? What was truly shocking was what could be seen beyond the broken glass. Or rather, what couldn't. Eggman hovered over to the shattered window, peering over its edge to get a proper assessment of the damage. From the hangar doors directly below the bridge, only about 100 meters or so of deck remained. The rest of it was simply... Gone. The detatched core area seemed to be sitting in a relatively large forest, with nothing but unnaturally tall trees in every direction the doctor could see, with the exception of a single stone tower, and what looked like a small town barely visible in the distance.

"HOW COULD THIS HAPPEN?!" Eggman shouted, "I thought the entire point of building a ship made out of jump-resistant material was to ensure that THIS WOULDN'T HAPPEN!"

"A-as I said, sir, the rupture was... Unexpected. The surge in energy, it was simply too much." ADAM watched as his master put his head in his hands, mourning the loss of his crowning masterpiece. "However, there IS good news, Master." ADAM then pulled up a schematic of the remainder of the ship, showing that much of the area surrounding the core was still intact. "Many vital facilities are still functional, and the troops are still largely unharmed. If we start now, we may be able to overcome his... Unfortunate delay."

Studying the hologram, Eggman's mood lightened when he realized his digital companion was correct. "You've got a point there, ADAM. I knew there was a reason I made you!"

"Um, thank you, sir?"

"Alright, first things first!" Eggman sat down in his Mobile and began formulating a plan of action. "The first thing to do is find life forms in order to establish what sort of world we've entered. I want all stealth troops on recon duty covering a 30 kilometer radi-"

"**IF ANYONE IS THERE, WE DEMAND THAT YOU SHOW YOURSELVES NOW!**" A loud, female voice pierced through the night.

On reflex, Eggman stood up, throwing his hands in the air. "I DIDN'T DO IT, OFFICER! I SWEAR!"

"Master?" ADAM said, "It appears the local life forms have found _us_."

* * *

Eh... I'm kinda iffy about how this one came out, but I hope you all enjoyed it!

-Lates!


	3. Out of Place

**Sorry this chap took so long****. Thanks to the people who liked the first couple chapters, you guys rock XD!**

**I wanted this to be the chapter where Sonic and RD meet, but it wound up being too long, so I had to cut out their scenes and move them to the next chapter. Sorry, but looks like things are gonna have to wait another chapter before becoming exciting, again... ^^'**

**Still, I hope you guys enjoy this chapter, anyways! So, without further ado, let's begin!**

* * *

**I still don't own Sonic or MLP... If only...**

* * *

SONIC: CHAOS AND HARMONY

_Chapter 3: Out of Place_

"Well, what do you think, Rarity?" Twilight asked.

In front of Twilight, a white unicorn stared through a magnifying glass at the glowing, green gem she'd found the night before. She stood up, brushing her long, purple curls to the side. "Well, Twilight, darling," the pony said in a very sophisticated accent, "as much as I was looking forward to sleeping in today, I'm glad you woke me up."

Twilight had to admit that, even in her sleep, it seemed like Rarity always had fashion on the brain. While she was no expert on the subject, Twilight could see that Rarity's nightgown had to be made of some very expensive fabric. How else would it look like real silver, yet still manage to fit her body like silk? Spike sure seemed to like it, that much was clear. Twilight was beginning to wonder if he'd even blinked since they walked in the door.

"I'm guessing that means you found something?"

Spike hopped up from his seat, finally deciding to stop gawking. "Is it valuable?"

"Quite the opposite, actually." Rarity said, putting her hands on her hips. "I couldn't find ANYTHING at all!"

Twilight raised an eyebrow. "What do you mean?"

Rarity then picked the emerald up off the table and began explaining her findings. "I mean that I know everything about every kind of gemstone on the planet; opals, rubies, amethyst, lapis, and even quarts, but this little rock is just one mystery after another!" Her words then started to become even more rushed and frantic, "Its mineral structure's unlike anything I've ever seen before, and although it doesn't appear to be cut, I've never seen a gem with this natural shape before, not to mention it must have some kind of special properties, because I can't use my magic to lift it up - something you yourself noted, Twilight - oh, and then there's the fact that - I'm not sure if you noticed, but -" she shoved it in Twilight's face for emphasis, "IT'S _GLOWING!_"

Twilight's head felt like it was spinning. The new information wasn't _that_ staggering, but Rarity had spoken like she was in an auction house, so a lot of it went over the purple unicorn's head.

Spike, on the other hand, was just plain confused. "So I _can't_ eat it?"

Twilight glared at him. "_Spiiiike_."

Rarity just smiled towards the young dragon and patted his head. "Believe me Spikey, dear, if I wasn't so sure eating this thing could kill you, I'd serve it to you with some rubies on the side." Spike beamed up at her at the mention of rubies. "Well, alright, maybe I wouldn't. But my point is, it could kill you, so don't try it." Spike frowned. Rarity turned her attention back to Twilight. "As for whether or not it's magical, I really can't say. Although that _does_ seem like the most likely explanation."

"Or aliens!" Spike piped up.

"Um... yes, that too. Where did you say this came from again, Twilight?"

"From a bright flash in the Everfree Forest last night," the purple Unicorn answered. "It just came flying through the window, like it was launched from a catapult!"

"I see..." Rarity said, still staring intently the emerald, "... There's one last thing I noticed." She then grabbed Twilight's hand, placing it on the the gem. "Do you feel that?"

Twilight nodded as she felt a strange, warm feeling move through her body. "Yeah, I noticed that, too."

"Let me feel!" Spike piped up, stretching his arm as much as he could to feel the emerald from below. Just from touching it with the tip of his finger, Spike immediately felt as if a wave of static electricity had passed through his body, instantly becoming a warm tingling. He withdrew his hand, and the feeling quickly vanished. "Whoa!" He said, lightly clutching his claw, "How are you two not more freaked out by that?"

"Because we're used to it, darling." Rarity answered.

Spike raised an eyebrow. "Huh?..."

"It's the same feeling we get when we use the Elements of Harmony," Twilight explained, "but at the same time, it feels... Different."

Spike reached up, pulling Rarity's hand down to where he could get a better look at it. "Sure doesn't look like an Element to me."

Rarity pulled her arm back up, cupping the gem with both hands. "Which is why I'd like to hold on to it for a little longer, if the both of you don't mind. I confess myself quite intrigued with it, and I'd like to see what I can find out. Not to mention, it's simply _gorgeous!_" Rarity was practically drooling at the mouth as she said that last statement.

Twilight nodded. "Sure, Rarity. Nopony knows gems better than you! Spike and I needed to go check on Fluttershy, anyways."

"Yeah," Spike mentioned with a sarcastic smirk, "_somepony's_ gotta go ply her off of her off of her ceiling boards after last night's light show."

"Oh dear," Rarity said, "I hadn't considered poor Fluttershy. Do give her my regards, would you?"

"Of course." Twilight said. "C'mon, Spike." The two then said their goodbyes (Spike adding an overly-dramatic "Until we meet again, my fair lady!") and walked out of Rarity's boutique down the path to Fluttershy's house.

"OH!" Rarity shouted at them as they left, "AND IF YOU FIND ANY MORE GEMS LIKE THIS, DON'T HESITATE TO BRING THEM TO ME!"

"WILL-DO." Twilight called back. She then turned to Spike as they continued walking. "Actually, I hadn't considered what else could've come from that flash in the woods last night. If that little green gem found its way all the way to our tree, I wonder what could've possibly wound up at Fluttershy's cabin?"

"Maybe she found a LIVE ALIEN!" Spike shouted, throwing his arms in the air.

Twilight let out a groan. "Spike, for the last time, there are NO-"_  
_

"Did somepony say LIVE ALIEN?!"

Twilight screamed and jumped back at the appearance of a young mare before them. "Pinkie Pie?!" Twilight asked, "Where did you come from?"

True to her name, Pinkie was pink from head to toe, from her bright pink body, to her soft, incredibly curly mane. Aside from that, she even wore pink-and-white striped armbands and socks. Her one-piece, yellow blouse/skirt with short, puffy sleeves was the only thing on her person that added any color variation at all. Well, that and the jean-shorts she wore underneath. The other thing that was clear to see just from looking at her was that she was brimming full with energy, as her eyes were almost bursting with excitement.

"Silly Twilight," Pinkie answered, "I always know when there's something exciting going on in Ponyville! Why just yesterday, I busted the mystery of the Breakfast Baked Goods Burglar!... It was me! They were SOOOO yummy!"

"Right..." Twilight said as she stood and began to dust herself off. It only took a moment for what Pinkie said to catch up with her. "Wait, you _stole_ baked goods?"

"Nah," Pinkie waved the question away, "I just forgot to pay for them. And don't worry, I paid for every last one once I caught me." So many questions. "But enough boring stuff; did somepony, or did somepony not, say something about aliens?"

Twilight opened her mouth to answer, but Spike interrupted, "There might be one at Fluttershy's house!"

"I KNEW IT!" Pinkie Pie shouted as she started bouncing up and down, "IKNEWITKNEWITKNEWIT!" She then grabbed Twilight and looked her in the eye, getting a little too close for comfort in the studious unicorn's opinion, "It's always been my _dream_ to meet a real life alien! Well, that and to eat my entire body weight in sweets! But I did that yesterday; Baked Goods Burglar, remember?"

"Yes, I remember," Twilight sighed, pulling her hyperactive friend's hands off her shoulders, "but Pinkie-"

"OH-OH-OH! Wouldn't it be awesome if he spoke the same language as us?! Oh, we would have SO MUCH to talk about! I bet we'd have a lot in common!"

"Well that much we can agree on, but Pinkie, I was just telling Spike that-"

"NO BUTS ABOUT IT!" Pinkie then jumped behind Twilight and pointed straight ahead dramatically, "Lead the way, Miss Sparkle! Route all power to rear-thrusters and FULL SPEED AHEAD!"

"ALL RIGHT!" Spike proclaimed, "Aliens _and_ Pinkie Pie! Now it's a PARTY!"

Twilight face-palmed. "Ugh... Fine," she groaned, "but I'm only going along with this to prove you both wrong. There's no such thing as aliens!"

**-o-o-o-**

"It's an alien, I tells ya!" Said a small, but loud voice.

"Dang-nabbit, Apple Bloom, there ain't no such thing as aliens!" came a louder voice, "It's probably just one'a Fluttershy's critters that got loose, that's all. Now quit findin' excuses and get back to helpin' us fix the barn!" Suddenly, there was a loud crashing noise, accompanied by splintering wood. "You okay in there, Big Mac?"

"Eyup!"

_What the heck is going on?_ Knuckles thought. His head was pounding, and he couldn't see anything around him. Who was talking? Why couldn't he see? _Oh, right,_ he thought, _my eyes are closed._ Well, one mystery solved. He opened his eyes to a blur of colors. It was an improvement, but not by much. Slowly, though, shapes started to form.

"I ain't never seen a critter that looked like this'n before!" The small voice protested, "And what's it doin' on our farm, anyhow? And right after our barn got totalled, fer that matter?"

Knuckles could now tell that he was laying face-up on the ground. The blurry green shapes he'd seen, he could now identify as apple trees, judging by the juicy, red fruits that dangled from their limbs.

"I ain't sure," the older-sounding voice answered the little one, "but right now, we got our hands full, so we can't worry about-is that critter movin'?"

Knuckles groaned as he pushed himself up. His limbs were sore, and his head was throbbing, but he wasn't sure which hurt worse. He held his large, gloved hand to his head, but it did little to stop the jolts of pain pounding at his skull.

"He's hurt!"

"APPLE BLOOM!"

Knuckles cracked his eyes open to look towards the sound of the voices. He saw two figures before him, both clearly female. One was small, yellow body and bright red hair, tied up in a big, pink bow. She appeared to be wearing denim overalls over a sleeveless, white tee-shirt. Behind her, he could see a long tail of red hair similar to that which was on her head, similarly tied in a bow. The larger being was orange in color, her sandy-blonde locks mostly being covered by a large cowboy hat. She wore a similar white tee to the smaller one, but instead of overalls, she wore a sandy brown jacket with matching pants, tied by a black belt around her waist. Knuckles took in the two females' appearances, the shape of their faces, their hoof-like feet, and their tails of hair falling behind them, and came to one conclusion: _Ponies?_...

The large one was currently holding the younger one by her arm, as if forbidding her from moving forward. "But Applejack," the small equine whined, "Fluttershy says you should always help a hurt critter in need. No matter what!"

The tall one, Applejack, gave an annoyed look. "Remind me to talk to her about that. And anyways, Apple Bloom, we don't know what this thing is! Fer all we know, it could eat fillies like you fer dinner!"

"Now yer just bein' silly, Sis!"

_"Applejack," "Apple Bloom," apple trees, what's with all the apples?_ Knuckles pushed himself up from the ground, only for a sudden pain in his leg to force him back down with a yelp. As he fell, he felt quite a lot of dirt fall off of his body. Curiously, he looked up at the ground in front of him to see that he was in a rather deep ditch, as if he'd landed after being launched from a giant sling-shot. That would certainly explain a few things._  
_

After a moment of trying to stand, he heard the elder sister sigh. "Alright, you win." Before he knew it, he felt himself being lifted up from his left side by a pair of powerful arms. He looked towards his aid to see Applejack hoisting him up. "We'll gett'em back to the house and see what we can do in ways'a patchin'em up, then it's right back to work, okay?"

"Thanks, Sis!" Apple Bloom cheered.

Knuckles looked at the older sister helping him up, only to see her shooting him a glare. "You'd better not be a filly-eater, or so help me..." She warned.

The red echidna couldn't help but chuckle a little at the pony's warning, though it came out as more of a cough. His chest was now beginning to hurt, just enough so to keep him from making a joking retort. Still, he appreciated the farm-pony's kindness, and actually found himself admiring her protectiveness of her little sister. Wherever he was, he was glad to have wound up somewhere as hospitable as this. Straining against what was possibly a broken rib, the injured guardian managed to force out a "Thank you."

Suddenly, Applejack stopped. Without warning, she jumped back and let go of Knuckles with a scream, making him buckle on his sore leg once more. He fell to his side, his head bumping firmly against a protruding tree root. And with that, his world went black once more. _Dammit..._

**-o-o-o-**

Sonic pushed himself upright as he opened his eyes. He could tell he was lying in the dirt, but why? At first, he could see nothing but grey blurs, but then his sight began to return. He then began to focus on his surroundings. All around him, he saw large, stone walls, littered with boulders and an occasional cave. If the hedgehog had to guess, he'd say he was in some kind of gorge. But how did he get here? The last thing he could remember...

Wait, what _was_ the last thing he remembered? Sonic began to think hard, trying to recall what he'd been doing before blacking out. _Was it something to do with Eggman?_ he thought. Suddenly, something clicked. "That's right!" He recalled aloud, "Me, Tails, and Knuckles were on Eggman's new battleship. What was it called? Whatever, not important." He then began to think harder, "I need to remember what happened before-"

Suddenly, a low growl from Sonic's right caught his attention. Turning towards the sound, Sonic stared at the entrance to a large cavern, as a foul-smelling wind erupted from its depths. Just then, he heard something moving within its depths, followed by the sound of scales scraping against stone.

"OH, BOY!" Sonic shouted, as he zipped out of the way, just as a large, red serpent erupted from its den to snap at him. Sonic braked a few feet away, turning to look at the creature that had nearly made a meal out of him. "Whoa... Heh-heh! Sorry, snakey, but you're too-WHOA!" He only had a second to react, launching himself into the air just as a second eel-like beast lashed out of its cavern to snap at him. "Too close!..." Sonic landed on the second creature's head, just long enough to launch himself off and use his powerful legs to start running up the canyon wall. "I gotta get out of this place!" the speedy hedgehog said as he defied gravity, "And it looks like the best route is up!"

However, Sonic barely made it a half-way up the wall before another red serpent erupted from its hole a few feet ahead. Startled by the creature's sudden appearance, Sonic quickly swerved out of the way, which was about twice as hard to do when fighting against gravity. Just as he thought he was in the clear, though, another serpent burst from its hole. He didn't have time to dodge this one, so he slammed on the brakes, hoping gravity would do the rest. It worked, and he began to fall backwards... Straight into the maw of another eel!

"Oh, COME ON!" he shouted. He reoriented himself to slide against the canyon wall, slowing his descent and giving him the leverage he needed to launch himself to the side. He landed on a narrow, stone outcropping that seemed to run along the canyon, before deciding to not take any chances and just run! As if on cue, eels started bursting out of their holes left and right, until it eventually looked like Sonic was outrunning a horizontal tidal wave of red.

"You've gotta be KIDDING!" he shouted, "_WHERE THE HECK AM I?!_"

* * *

**Well, there you have it! I'm still not sure I got Rarity and Pinkie quite right, but the Apples were fun to write for.**

**Again, sorry for the wait, guys. And I promise to get the next chapter out a lot sooner!**


End file.
